Sheppard the Sheppard
by Inu-yokia- princess
Summary: On Hold:On a mission to find an ancient device the team is ambushed by the Wraith. In the struggle John is pushed into a device and it activates. Now the whole base thinks Rodney's crazy and he is Sheppards only hope of getting back to normal.
1. Chapter 1

Sheppard the Sheppard

By Inu-yokia-princess

Disclaimer: Stargate Atlantis and it's characters are not mine.

(A/N: this would be my very first attempt at a Stargate Atlantis fanfiction as well as my first slash fic. I apologize for my grammar and the many OOC moments. Please read and enjoy. Also I respectfully ask that only constructive criticism be allowed and no flames. Also would anyone be interested in betaing this story for me? Thank you.)

John flew across the room crashing into the dark walls of the ancient lab. The Wraith had beaten them to this particular lab on the planet P5982. They had discovered the planet in the database and it had mentioned a very powerful and important device that was hidden within the lab. However the Wraith had already been searching the planet and come up with nothing. Of course the team had no clue the Wraith were already in the underground lab so they were naturally surprised to be ambushed.

John held his head as he picked himself up to punch at the attacking Wraith. His gun had fallen away from him when he hit the wall with a powerful force. The Wraith was hit in the stomach by one of John's fists only to pick John up with a yell and throw him half way across the room. Teyla yelled out to him as she kept shooting at an attacking Wraith. John landed with a thud against some sort of button.

The wall began to glow the blue light of an ancient device. A shock similar to the one that hit Rodney when he got telekinetic powers from that ascension device hit John. The color this time was a purple that seemed to go to a light pink. His body shook for a moment until he fell limp. Rodney who was the closets to him frantically shot at the attacking Wraith as he yelled out to John attempting to get a reaction from John's limp body.

John stirred and opened his eyes to find smoke that only worsened his blurry vision. Within the following minutes there was a lot of commotion and soon he found himself being lifted on the strong shoulder of Ronon. John wasn't sure how long he was unconscious or when he had lost consciousness, but he awoke in the medical bay with a pounding head ache that made him swear under his breath. He looked around noting that no one was at the readily available to tell him what was going on. Mentally John checked for his body for aches and injuries. Finding that he only had one large bump on the back of his head and a bruise here and there, John looked around and noticed Rodney coming towards him. Rodney stopped and blinked before running to John and frantically yelling in his radio that John was awake.

The next few minutes were spent with Doctor Keller checking him over and his friends coming to see him. Mr. Woolsey was in for a few moments to say hello and tell him that he would get a few days of recovery before he expected his mission report. John sighed as he realized he had no idea what had occurred the last thing he recalled was being hit with a strange purple light.

Teyla and Ronon came up to him after most of the commotion was done with. Teyla held his hand as she looked at him with her gentle eyes. Ronon also stood close by arms folded around his chest. Rodney was on the other side of his bed looking out of place and unsure. John's first line of business was to find out what happened to him. "Alright now would someone tell me what is going on here?" John asked looking at each of his team to give him an answer.

"We were in a great battle with the Wraith one that was hard and difficult. We barley managed to escape. You were hit by a Wraith into a strange machine that caused you to be unconscious. The fight was hard and long, we escape under a smoke cover from Ronon shooting his gun at one of the devices on the wall. We were out numbered and you were injured we had no choice but to retreat." Teyla explained in a soothing voice. Doctor Keller had cleared him with a bill of full health however Teyla still felt uneasy.

"Wonderful, now that your declared fine I have work to do." Rodney excused himself seeming to be a bit bothered. John stared at Rodney's retreating form in a moment of worry. This moment ended up causing John to look back at Teyla and shake his head. The three spoke for around an hour informing John he had been out for at least three days and one rather strange scientist refused to leave him for more than an hour at a time. John could see the amusement in Ronon's eyes as he told John of this. Ronon had found it funny that their resident asshole of a genius was so overly worried about there commanding officer who he so often fought with.

John at last was cleared to be set free from his medical bed and he practically jumped up to get out of the sick bay as fast as he could. John was somehow still bone tired but he knew he wouldn't be able to sleep, not yet at least. The first thing on his list was to visit a certain scientist. With a determined look John ran right to the lab where are those scientist geeks seemed to live in. He could already hear them all working away and heard what was unmistakably Rodney arguing away with Zelenka.

John suddenly felt strange hearing the arguing Zelenka and Rodney and thinking to himself that it sounded a lot like they were having some form of fun. John took a breath before schooling his features into his best lets torture Rodney face. Yes John had grown use to using an amused face when ever present in Rodney's lab as the frustration and annoyance that oozed out of the scientist would often widen his smile.

Before John could open the door a rather flustered and annoyed Zelenka stormed out nearly plowing into the slightly surprised colonel. John watched Zelenka rush away rambling curses. Walked into the lab to see the other scientists busy at work by now far too use to this to let it even begin to bother them. John's vision focused on Rodney, he was red in the face and seemed slightly out of breath from what John was sure was a long rant without taking a breath.

Rodney stared at John and immediately calmed down taking a deep breath to stop himself from ranting on further. Rodney eyed John for a moment wondering what he was up to this time. "So released from the infirmary at last. Everyone has been nuts since we brought you back knocked out. Do you know how..." the words trailed off as Rodney looked at John whose brow now furrowed. "At any rate I have important work to do so either speak or leave me be." Rodney quickly looked back to his hand held computer tablet and started up a program apparently at random.

John simply stared at Rodney; he was going to make a good come back but decided against it. Suddenly he was very tired and wanted a good nights rest. With a quick glance at the busy Rodney, John wandered back to his quarters. The door opened with a swish of his arm he stripped himself of everything but his boxers leaving his clothing in a lump on the floor. John found that as soon as his head hit his bed he was fast asleep.

John awoke curled in a small ball. A strange sleeping potion in deed for him since he most commonly slept on his side or back. Occasionally he slept on his stomach, never had he found himself curled in a ball. He got up and pulled his arms out far above his head. That was when John noticed something wasn't right. He looked up to see paws instead of hands. John on high alert got up from his bed and ran on all fours to the bathroom mirror, with some difficulty opening the door. His was still able to open things apparently he just needed to jump to reach what passed for a door knob in Atlantis now.

What John saw in the mirror freaked him out more than the fact that he now has paws. Facing back at the colonel was a tan and black German Sheppard. John's military training forced him not to panic. He took in a deep breath and ran out in search of someone anyone that could somehow help him.

As soon as he walked through the door he ran the names of people through his skull. Woolsey was out of the question, chances were he would be shot without even a chance to explain himself. Ronon was most likely not a good idea with his instincts. Doctor Keller may be a good idea once he explains to another person. Teyla wasn't too bad of an idea either though even she may not understand him. John wasn't even sure if he could still be able to be understood by humans. Rodney stayed in his mind as he knew that even though Rodney was a genius about fixing these issues this one would probably be better for Teyla first, however John felt himself lean towards Rodney first.

As soon as his mind was made up John ran as fast as his paws would take him which John noted almost happily that was a great deal faster than his human form. He found himself at Rodney's lab which thanks to John's new found smelling abilities he found Rodney was inside. He scratched at the door before choosing to open the door jumping again. At last the door opened and the only one in the lab seemed to be Rodney. In fact Rodney was the only one other than a scatter of people he had seen all day. It was still very early so it wasn't all that surprising to see that Rodney was fast asleep most likely was up till recently working. John's ears twitched a moment and his tail wagged in amusement. Instead of yelling or perhaps barking he choose to go up next to Rodney and nudge his hand. He also threw in a lick for the affect. Rodney sprang awake screaming and jumped a mile causing John's tail to wag even harder than it had been previously, obviously enjoying this.

"What are you doing here? How are you here?" Rodney rambled trying to make sense of this. He hadn't seemed as surprised as John thought he would be. Rodney continued to ramble in long sentences at a speed that couldn't possibly be healthy.

In order to stop the barley breathing Rodney John soon found himself speaking. "Rodney calm down already!" to John's ears he found that he sounded as he did. Apparently he sounded the same to Rodney too. Rodney stood for about ten minutes silent which freaked out John who had never heard Rodney so quiet unless asleep or knocked out.

Rodney regained himself and blinked "Sheppard?" he stared at the dog trying as hard as possible to believe what he just heard. Had he just heard this dog speak in the voice of the colonel?

"Yes Rodney, I don't know how I got like this but I am." Before any other words could be exchanged Zelenka came into the room and stared at Rodney then John not sure what to say.

"Well now I have two people who can help." John stated. But he found that Zelenka was acting strangely. The next thing he knew he was eye level with the man.

"What a beautiful animal." Zelenka stated as he pat John on the head. John suddenly found himself happy for the petting, however he felt like glaring at the beautiful animal part.

"Okay yes pretty doggie now help Rodney fix me!" John said as he felt Zelenka hit a soft spot and his leg began to twitch in happiness.

"What a good dog. How did you bring him here Rodney?" Zelenka asked staring up at Rodney to get an answer.

Rodney stared back all he could seem to do was watch. He opened his mouth and the words flew out in a rushed tone. "What are you talking about that's Sheppard can't you hear him?!"

Zelenka gave Rodney a look that spoke volumes. As one Rodney and John realized that the only one who was able to understand John was Rodney and they had to convince everyone on base that Rodney wasn't completely crazy.

(Alright this was my attempt at a comedy that will lead to a very fluffy romance. I would appreciate it if someone of more than one person would tell me if this is a project worth considering continuation. Please give only constructive advice with as little malice as possible. Now please review and tell me what you think.)


	2. Chapter 2

Shepard the Shepard

By inu-yokia-princess

(A/N: Thank you all who reviewed and encouraged me to continue. Now John and Rodney is going to be the main relationship I do plan on a slight Zelenka and Rodney, also I plan to touch on Rodney and Jennifer, however the result will still be McShep. Again I apologize for my horrid grammar mistakes and I hope that you will still enjoy this story despite my inadequate writing. Please read and review.)

Disclaimer: I do not own Stargate Atlantis

Zelenka looked at Rodney for a moment then he looked at "John". "Rodney there is no need for you to make up such things. I understand bringing a earthly animal to Atlantis isn't a normal thing to do and is most likely against regulations, however I can understand." Zelenka told Rodney continuing to scratch the depressed John's ears.

Rodney sighed unable to stop himself. He realized Zelenka was not going to believe him no matter what he said. So Rodney choose to glare at the mousy scientist. "Alright fine, you know what I'm going to find someone else who can help!" with a quick glare Rodney went out of the lab in search of Doctor Keller.

John stared at the retreating back of Rodney and decided as good as being scratched behind the ears was he knew that Rodney was the key to getting back to normal. With his mind made up John ran after his main scientist. He found him just about to enter the medical bay.

Doctor Keller was the only one there at the time John noted realizing it was still extremely early. "Rodney? Awww what a cute dog!" again John was being scratched behind the ears and in a slight heaven.

"No not cute dog. That dog is Sheppard, now I don't know why but I can understand him and I think it has to do with that device that hit him." Rodney began with a sinking feeling that maybe Jennifer wasn't the best first choice with only his word to back himself up.

Jennifer looked up at Rodney for a moment. She noticed how worried he appeared and turned her attention to "Sheppard" he looked like an every day dog to her. How the dog was brought to Atlantis she did not know, but she did know that what Rodney was suggesting no matter how crazy and unthinkable this was Atlantis.

"Yes I know its crazy but crazier things have happened." Rodney thought for a moment and realized as crazy as the last five years had been, he doubted anything this crazy had ever occurred. "Look take a DNA sample and see if any of it matches. After all he can still open doors so he must still have the gene." Rodney ran out of the medical bay without another word, leaving John alone with the good doctor.

Rodney immediately went back to his lab to wait and see the results. As he entered the lab he noticed that Zelenka was giving him a rather strange look. Rodney ignored this the only way he could by getting to work. Which soon enough resulted in an argument with the mousy scientist that seemed to calm Rodney down.

The lunch room was filled with people as everyone began to wake up. One such person was Doctor Jennifer Keller who sat down at the table containing Teyla and Ronon. She had grabbed a fruit salad and some milk that she barley touched. She was waiting on the test to come back and she also had to worry about what she would do if the test came back and it was or wasn't Shepard. "Doctor Keller is everything alright?" Teyla asked concern in her voice.

"Yea, I'm just a bit concerned. Rodney came in this morning and asked me to do a DNA test on a German Shepard, a type of animal on our planet, claiming that he was colonel Sheppard." Jennifer looked at her friends in mild distress, letting the news sink into their skulls she attempted to eat a strawberry from her fruit salad.

"That is strange news indeed." Teyla stated her forehead showing signs of concern. She turned to Ronon to see what his reaction was. She was rewarded with a raised eye brow.

"What McKay's finally lost it?" Ronon didn't seem as afraid as Jennifer or Teyla was to voice what they all were thinking.

"Well I don't know. He hasn't slept much since John was brought back unconscious. He didn't leave John's side for more than an hour. It's possible that the lack of sleep and his stress over what happened is causing him to be delusional." Jennifer stated her theories that she had come up with.

"So what do we do? Rodney is very intelligent and needed member of our team. If he is sick we must help him." Teyla responded now more worried than before. She looked at Ronon to see even he was a little worried. They all had been when Sheppard was hit by that purple beam, though Rodney seemed most affected by it.

"I don't know. Rodney looked as though he was still attempting to convince himself of what he was saying while trying to convince me as well." Just as Jennifer was about to continue she got a page telling her the results had come in. "Well lets see if Rodney is really crazy or not."

With that the three left for Jennifer's lab. When the results came Jennifer looked astonished. "This is an almost exact match to colonel Sheppard." The look on the Doctor's face was priceless. She could barley believe what she was looking at. Rodney was right.

As soon as Rodney heard that he was not going crazy he relaxed for all two seconds before dropping everything and running to the medical bay. "Well it's a bout time." John stated when he saw Rodney run through the door.

"Well forgive me for not wanting to be looked at like I was crazy!" Rodney shot back. He was rewarded with the very look he was trying to avoid. "You said you believed me!" Rodney stared desperately.

"We do. It's just that, you're the only one who can apparently understand what the colonel is saying." Teyla soothed. She was a bit shocked to hear the dog that was proven to be her team leader bark and have Rodney respond.

"Yes I don't know why but I can. Now this has to do with that device, we have to go back for it." Rodney suddenly began to pace thinking of a way to collect the device if the Wraith possibly took it when they left.

"Yes the device is most likely responsible but you all barley got out of there with your lives. And you have to go through Woolsey." Jennifer had seen Rodney in a panic before, but this seemed different.

"What has to go through me? I received word that I was needed in the medical." Woolsey cut himself off as he noticed Sheppard for the first time. "Who brought a dog here? That is a violation and the dog must be taken at once." Woolsey looked at John almost longingly for a moment as if tempted to do what almost everyone did when they first saw John pet him.

"This isn't your normal dog Mr. Woolsey." Teyla began unsure on how to tell the man that one of his key colonels was turned into a dog by a device that they had no idea where it was or what it was suppose to do.

"It's Sheppard." Ronon ever the blunt one told him. His face as always gave no sigh of any amusement. The look on Mr. Woolsey's face told everyone that like the rest of them, he didn't want to believe it.

"Ronon is right. The DNA is a complete match to that of Colonel John Sheppard. Though I admit this is very hard to believe, but Rodney can understand him still." Everyone turned to look at Rodney who was standing next to John who looked up at him as well.

John suddenly realized that Rodney was the only one out of everyone that hadn't petted him on first sight. Even Ronon scratched him behind the ears when no one was looking. John wasn't sure why but that bothered him.

"If what you say is true, then we have to find a way to fix this." Mr. Woolsey was still unsure, he had been in command at Atlantis for only a few months and he had heard and read the reports of how crazy things on a Stargate base could get, yet never had he heard of something this bizarre. "How do we fix this?"

"Well I have a theory, but it involves getting that device that hit Sheppard. Now that's either still on the planet if we are lucky, or if the fates choose to hate us as they so often do the Wraith took it and we have no way of knowing where they went or how to get to that place." Rodney responded, he sounded strained as he tried to think of a way to fix this. He knew that if they could just get a hold of that device they could figure this all out.

"So you want me to give you permission to go back to the planet and look for it, when you barley escaped the last time you went there?" Woolsey only sounded shocked by this, by now he was more than use to the idea of his teams going into dangerous places for the sake of saving one of more lives. "You have a go, and you'll have to take him with you as well."

Everyone was shocked that Mr. Woolsey was so willing to let them go, normally he would at least pretend to not want them to, but what shocked them most of all was that John was being allowed to come along in his state. "Thank you Mr. Woolsey." Teyla snapped out of it the fastest and thanked him, she could sense that Mr. Woolsey was worried as well.

"So you think you can handle this?" Ronon asked he looked at John who barked at him in almost a growl. Ronon didn't know what John just said but he knew that it would put a smirk on his face and make him proud to call Sheppard a friend. Ronon stared at Rodney waiting to have what John said translated to him.

"He said, let's just get going." Rodney waited a moment "He also added a growl in for a yes I can I believe." Rodney translated staring at the dog at his side. If anyone had told him yesterday that he would be the only one able to understand Sheppard when he was in dog mode he would have laughed in their faces and said something along the lines of you have some imagination.

Without so much as another word Teyla and Ronon left to get their gear. Rodney looked at Sheppard for a moment and then signaled him to follow. Curiously John followed Rodney wondering what could possibly be going on in the scientist's head.

Within an hour the team was assembling in front of the gate. The only two missing were Rodney and John from the group. Teyla and Ronon shared a look of worry for a moment before looking to watch for them coming. A second team was going with them for back up this time, hopefully however they would not need it.

John and Rodney approached them both in gear. John was in a vest that looked like it was carrying supplies and made just for him. He looked determined as ever his teeth bearing every now and again to show just how ready he was. Rodney stood beside him looking less prepared and more worried about what would await.

The gate burst into life and the teams set out for the planet, each hoping what they were looking for would still be there and not on board a Wraith ship.

(A/N: That's it for this chapter. I'm hoping that I will be able to finish the next chapter by next week and have it uploaded then too. Thanks to all those who reviewed.)


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